tbuckley/cabot-search huggingface dataset:
Reply
Authors: Hang Shi, Liqing Yu
Journal: Hepatology (2022)

The letter by Luo et al. raised some critiques about our paper1 reporting genetic evidence for adipose lipolysis as a critical player in alcohol‐associated liver disease (ALD) pathogenesis in the National Institute on Alcohol Abuse and Alcoholism (NIAAA)'s murine model of chronic plus binge ethanol feeding.2 We addressed the critiques as follows. Age difference between male and female mice. The reason we used different ages for males and females was that males are heavier than females of the same age and ethanol feeding often causes weight loss and hypothermia in younger and lighter mice, leading to increased mortality. This practice was described in the original NIAAA protocol.2 The age difference between two sexes should not affect our conclusions because all parameters were compared within groups of the same sex. Baseline difference in aspartate aminotransferase (AST) and alanine aminotransferase (ALT). AST and ALT are markers of liver injury. We never stated that adipose lipolysis deficiency protects against liver injury. Our primary conclusion was that ethanol induces fatty liver and oxidative stress in an adipose lipolysis‐dependent manner. Factors affecting fatty liver, such as initial hormone levels, BMI, and primary disease. These factors are considered in human but not rodent studies. Body mass index (BMI) is a measure of obesity in humans but not rodents. We clearly showed that ethanol feeding induces fatty liver, oxidative stress, and liver injury in healthy inbred mice. When using inbred mice, a group of four or more is well accepted in many assays in the field because this sample size can often give enough statistical power. Feeding pattern concern. We followed exactly the original protocol of the NIAAA model.2 We did pair‐feeding. Food and energy intake remained the same among all groups. Because ethanol‐fed mice usually consume less amounts of food than those on the control diet, a reduced amount of control diet was given to control mice as per NIAAA protocol.2 A mild weight loss, despite statistically significant, is not surprising because of pair‐feeding and the change of diet forms (solid to liquid). This ALD model has been widely employed in the field of ALD. Diagnostic criteria for fatty liver. Unlike human studies that normally adopt pathological diagnostic criteria for fatty liver, this was a rodent study. We quantified degrees of hepatic fat deposition by biochemical and morphological approaches, a standard practice for characterizing rodent fatty liver. Relevance to ALD. We used the well‐accepted NIAAA model2 in the study and believe our findings are highly relevant to ALD pathogenesis.
Multiomics characterization of mouse hepatoblastoma identifies yes‐associated protein 1 target genes
Authors: Tomás C. Rodríguez, Suet‐Yan Kwan, Jordan L. Smith, Sina Dadafarin, Chern‐Horng Wu, Erik J. Sontheimer, Wen Xue
Journal: Hepatology (2022)

Background and Aims: Hepatoblastoma (HB) is the most common primary liver malignancy in childhood and lacks targeted therapeutic options. We previously engineered, to our knowledge, the first yes‐associated protein 1 (YAP1) S127A –inducible mouse model of HB, demonstrating tumor regression and redifferentiation after YAP1 withdrawal through genome‐wide enhancer modulation. Probing accessibility, transcription, and YAP1 binding at regulatory elements in HB tumors may provide more insight into YAP1‐driven tumorigenesis and expose exploitable vulnerabilities in HB. Approach and Results: Using a multiomics approach, we integrated high‐throughput transcriptome and chromatin profiling of our murine HB model to identify dynamic activity at candidate cis ‐regulatory elements (cCREs). We observed that 1301 of 305,596 cCREs exhibit “tumor‐modified” (TM) accessibility in HB. We mapped 241 TM enhancers to corresponding genes using accessibility and histone H3K27Ac profiles. Anti‐YAP1 cleavage under targets and tagmentation in tumors revealed 66 YAP1‐bound TM cCRE/gene pairs, 31 of which decrease expression after YAP1 withdrawal. We validated the YAP1‐dependent expression of a putative YAP1 target, Jun dimerization protein 2 (JDP2), in human HB cell lines using YAP1 and LATS1/2 small interfering RNA knockdown. We also confirmed YAP1‐induced activity of the Jdp2 TM enhancer in vitro and discovered an analogous human enhancer in silico. Finally, we used transcription factor (TF) footprinting to identify putative YAP1 cofactors and characterize HB‐specific TF activity genome wide. Conclusions: Our chromatin‐profiling techniques define the regulatory frameworks underlying HB and identify YAP1‐regulated gene/enhancer pairs. JDP2 is an extensively validated target with YAP1‐dependent expression in human HB cell lines and hepatic malignancies.
TimeTree 5: An Expanded Resource for Species Divergence Times
Authors: Sudhir Kumar, Michael Suleski, Jack M Craig, Adrienne E Kasprowicz, Maxwell Sanderford, Michael Li, Glen Stecher, S Blair Hedges
Journal: Molecular Biology and Evolution (2022)

Abstract We present the fifth edition of the TimeTree of Life resource (TToL5), a product of the timetree of life project that aims to synthesize published molecular timetrees and make evolutionary knowledge easily accessible to all. Using the TToL5 web portal, users can retrieve published studies and divergence times between species, the timeline of a species’ evolution beginning with the origin of life, and the timetree for a given evolutionary group at the desired taxonomic rank. TToL5 contains divergence time information on 137,306 species, 41% more than the previous edition. The TToL5 web interface is now Americans with Disabilities Act-compliant and mobile-friendly, a result of comprehensive source code refactoring. TToL5 also offers programmatic access to species divergence times and timelines through an application programming interface, which is accessible at timetree.temple.edu/api. TToL5 is publicly available at timetree.org.
Bending oxygen saturation index and risk of worsening heart failure events in chronic heart failure
Authors: Rafael de la Espriella, Martina Amiguet, Gema Miñana, Juan Carlos Rodríguez, Patricia Moyano, Daniel Segarra, Julio Fernández, Enrique Santas, Gonzalo Núñez, Miguel Lorenzo, Clara Bonanad, Edgardo Alania, Alfonso Valle, Juan Sanchis, Vicent Bodí, Jose Luis Górriz, Jorge Navarro, Pau Codina, Adriaan A. Voors, Antoni Bayés‐Genís, Julio Núñez
Journal: European Journal of Heart Failure (2022)
Maintaining genomic surveillance using whole-genome sequencing of SARS-CoV-2 from rapid antigen test devices
Authors: Genevieve E Martin, George Taiaroa, Mona L Taouk, Ivana Savic, Jacinta O'Keefe, Robert Quach, Jacqueline Prestedge, Marcelina Krysiak, Leon Caly, Deborah A Williamson
Journal: The Lancet Infectious Diseases (2022)
Multimodal imaging of capsid and cargo reveals differential brain targeting and liver detargeting of systemically-administered AAVs
Authors: Jai Woong Seo, Javier Ajenjo, Bo Wu, Elise Robinson, Marina Nura Raie, James Wang, Spencer K. Tumbale, Pablo Buccino, David Alexander Anders, Bin Shen, Frezghi G. Habte, Corinne Beinat, Michelle L. James, Samantha Taylor Reyes, Sripriya Ravindra Kumar, Timothy F. Miles, Jason T. Lee, Viviana Gradinaru, Katherine W. Ferrara
Journal: Biomaterials (2022)
Reply to Yuxuan Song, Yiqing Du, and Tao Xu’s Letter to the Editor re: Matthew Mossanen, Filipe L.F. Carvalho, Vinayak Muralidhar, et al. Genomic Features of Muscle-invasive Bladder Cancer Arising After Prostate Radiotherapy. Eur Urol 2022;81:466–73
Authors: Filipe L F Carvalho, Matthew Mossanen, Eliezer M Van Allen, Kent W Mouw
Journal: European Urology (2022)
Development of a score for early identification of children with Kawasaki disease requiring second-line treatment in multi-ethnic populations in Europe: A multicentre retrospective cohort study
Authors: Naim Ouldali, Rosa Maria Dellepiane, Sofia Torreggiani, Lucia Mauri, Gladys Beaujour, Constance Beyler, Martina Cucchetti, Cécile Dumaine, Adriano La Vecchia, Isabelle Melki, Rita Stracquadaino, Caroline Vinit, Rolando Cimaz, Ulrich Meinzer
Journal: The Lancet Regional Health - Europe (2022)

Early identification of high-risk patients is essential to stratify treatment algorithms of Kawasaki disease (KD) and to appropriately select patients at risk for complicated disease who would benefit from intensified first-line treatment. Several scores have been developed and validated in Asian populations but have shown low sensitivity in predicting intravenous immunoglobulin (IVIG) resistance in non-Asian populations. We sought methods to predict the need for secondary treatment after initial IVIG in non-Asian populations.We conducted a retrospective, multicenter study including consecutive patients with KD admitted to two tertiary pediatric hospitals in France and Italy from 2005 to 2019. We evaluated the performance of the Kawanet-score and compared it with the performances of initial echocardiography findings, and of a newly proposed score combining the Kawanet-score and initial echocardiography findings. For each score, we assessed the AUC, sensitivity and specificity for predicting the need for second-line treatment.We included 363 children with KD, 186 from France and 177 from Italy, of whom 57 (16%) required second-line therapy after the first IVIG dose. The Kawanet score, coronary artery dilation or aneurysm with maximal Z-score ≥2.0 at baseline, and abnormal initial echocardiography had a sensitivity of 43%, 55% and 65% and a specificity of 73%, 78%, 73%, respectively, for predicting the need for second-line treatment. The Kawanet-score was significantly improved by combining it with initial echocardiography findings. The best predictive performance (Sensitivity 76%, Specificity 54%) was obtained by combining the Kawanet-score with abnormal initial echocardiography, defined by the presence of either coronary artery maximal Z-score ≥2.0, pericarditis, myocarditis and/or ventricular dysfunction. This score predicted the need for second-line treatment in European, African/Afro-Caribbean and Asian ethnicity with a sensitivity of 80%, 65% and 100%, respectively, and a specificity of 56%, 51% and 61%, respectively.Our study proposes a score that we named the Kawanet-echo score, which allows early identification of children with KD who require a second-line treatment in multi-ethnic populations in Europe.None.
Reply to Andreas Skolarikos’s Words of Wisdom re: Effect of Robot-assisted Radical Cystectomy with Intracorporeal Urinary Diversion vs Open Radical Cystectomy on 90-Day Morbidity and Mortality Among Patients with Bladder Cancer: A Randomized Clinical Trial. Eur Urol. In press
Authors: James W F Catto, Pramit Khetrapal, Gareth Ambler, Norman R Williams, Chris Brew-Graves, John D Kelly
Journal: European Urology (2022)
Re: Sarah P. Psutka, Roman Gulati, Michael A.S. Jewett, et al. A Clinical Decision Aid to Support Personalized Treatment Selection for Patients with Clinical T1 Renal Masses: Results from a Multi-institutional Competing-risks Analysis. Eur Urol 2022;81:576–85
Authors: Mike Wenzel, Felix K-H Chun, Andreas Becker
Journal: European Urology (2022)
Engineering the viscoelasticity of gelatin methacryloyl (GelMA) hydrogels via small “dynamic bridges” to regulate BMSC behaviors for osteochondral regeneration
Authors: Changjiang Liu, Qifan Yu, Zhangqin Yuan, Qianping Guo, Xiting Liao, Feng Han, Tao Feng, Guoping Liu, Runze Zhao, Zhuang Zhu, Haijiao Mao, Caihong Zhu, Bin Li
Journal: Bioactive Materials (2022)

The dynamic extracellular matrix (ECM) constantly affects the behaviors of cells. To mimic the dynamics of ECM with controllable stiffness and energy dissipation, this study proposes a strategy in which a small molecule, 3,4-dihydroxybenzaldehyde (DB), was used as fast "dynamic bridges'' to construct viscoelastic gelatin methacryloyl (GelMA)-based hydrogels. The storage modulus and loss modulus of hydrogels were independently adjusted by the covalent crosslinking density and by the number of dynamic bonds. The hydrogels exhibited self-healing property, injectability, excellent adhesion and mechanical properties. Moreover, the in vitro results revealed that the viscous dissipation of hydrogels favored the spreading, proliferation, osteogenesis and chondrogenesis of bone marrow mesenchymal stem cells (BMSCs), but suppressed their adipogenesis. RNA-sequencing and immunofluorescence suggested that the viscous dissipation of hydrogels activated Yes-associated protein (YAP) by stabilizing integrin β1, and further promoted nuclear translocation of smad2/3 and β-catenin to enhance chondrogenesis and osteogenesis. As a result, the viscoelastic GelMA hydrogels with highest loss modulus showed best effect in cartilage and subchondral bone repair. Taken together, findings from this study reveal an effective strategy to fabricate viscoelastic hydrogels for modulating the interactions between cells and dynamic ECM to promote tissue regeneration.
Reply to Meny Lv, Xufei Luo, and Yaolong Chen’s Letter to the Editor re: Mauro Gacci, Vasileios I. Sakalis, Markos Karavitakis, et al. European Association of Urology Guidelines on Male Urinary Incontinence. Eur Urol. In press. https://doi.org/10.1016/j.eururo.2022.05.012
Authors: Mauro Gacci, Vasileios I Sakalis, Markos Karavitakis, Stavros Gravas
Journal: European Urology (2022)
Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy
Authors: Kathryn E. McCauley, Elze Rackaityte, Brandon LaMere, Douglas W. Fadrosh, Kei E. Fujimura, Ariane R. Panzer, Din L. Lin, Kole V. Lynch, Joanna Halkias, Ventura F. Mendoza, Trevor D. Burt, Casper Bendixsen, Kathrine Barnes, Haejin Kim, Kyra Jones, Dennis R. Ownby, Christine C. Johnson, Christine M. Seroogy, James E. Gern, Homer A. Boushey, Susan V. Lynch
Journal: Cell Reports Medicine (2022)

Maternal asthma status, prenatal exposures, and infant gut microbiota perturbation are associated with heightened risk of atopy and asthma risk in childhood, observations hypothetically linked by intergenerational microbial transmission. Using maternal vaginal (n = 184) and paired infant stool (n = 172) samples, we identify four compositionally and functionally distinct Lactobacillus-dominated vaginal microbiota clusters (VCs) that relate to prenatal maternal health and exposures and infant serum immunoglobulin E (IgE) status at 1 year. Variance in bacteria shared between mother and infant pairs relate to VCs, maternal allergy/asthma status, and infant IgE levels. Heritable bacterial gene pathways associated with infant IgE include fatty acid synthesis and histamine and tryptophan degradation. In vitro, vertically transmitted Lactobacillus jensenii strains induce immunosuppressive phenotypes on human antigen-presenting cells. Murine supplementation with L. jensenii reduces lung eosinophils, neutrophilic expansion, and the proportion of interleukin-4 (IL-4)+ CD4+ T cells. Thus, bacterial and atopy heritability are intimately linked, suggesting a microbial component of intergenerational disease transmission.
Seroprevalence and infection fatality rate of the SARS-CoV-2 Omicron variant in Denmark: A nationwide serosurveillance study
Authors: Christian Erikstrup, Anna Damkjær Laksafoss, Josephine Gladov, Kathrine Agergård Kaspersen, Susan Mikkelsen, Lotte Hindhede, Jens Kjærgaard Boldsen, Signe Winther Jørgensen, Steen Ethelberg, Dorte Kinggaard Holm, Mie Topholm Bruun, Janna Nissen, Michael Schwinn, Thorsten Brodersen, Christina Mikkelsen, Susanne Gjørup Sækmose, Erik Sørensen, Lene Holm Harritshøj, Bitten Aagaard, Khoa Manh Dinh, Michael P. Busch, Charlotte Sværke Jørgensen, Tyra Grove Krause, Henrik Ullum, Sisse Rye Ostrowski, Laura Espenhain, Ole Birger Vesterager Pedersen
Journal: The Lancet Regional Health - Europe (2022)

Introduction of the Omicron variant caused a steep rise in SARS-CoV-2 infections despite high vaccination coverage in the Danish population. We used blood donor serosurveillance to estimate the percentage of recently infected residents in the similarly aged background population with no known comorbidity.To detect SARS-CoV-2 antibodies induced due to recent infection, and not vaccination, we assessed anti-nucleocapsid (anti-N) immunoglobulin G (IgG) in blood donor samples. Individual level data on SARS-CoV-2 RT-PCR results and vaccination status were available. Anti-N IgG was measured fortnightly from January 18 to April 3, 2022. Samples from November 2021 were analysed to assess seroprevalence before introduction of the Omicron variant in Denmark.A total of 43 088 donations from 35 309 Danish blood donors aged 17-72 years were screened. In November 2021, 1·2% (103/8 701) of donors had detectable anti-N IgG antibodies. Adjusting for test sensitivity (estimates ranging from 74%-81%) and November seroprevalence, we estimate that 66% (95% confidence intervals (CI): 63%-70%) of the healthy, similarly aged Danish population had been infected between November 1, 2021, and March 15, 2022. One third of infections were not captured by SARS-CoV-2 RT-PCR testing. The infection fatality rate (IFR) was 6·2 (CI: 5·1-7·5) per 100 000 infections.Screening for anti-N IgG and linkage to national registers allowed us to detect recent infections and accurately assess assay sensitivity in vaccinated or previously infected individuals during the Omicron outbreak. The IFR was lower than during previous waves.The Danish Ministry of Health.
Multifunctional nanolocks with GSH as the key for synergistic ferroptosis and anti-chemotherapeutic resistance
Authors: Jiawei Zhu, Xiaorui Wang, Yan Su, Jinjun Shao, Xuejiao Song, Wenjun Wang, Liping Zhong, Lu Gan, Yongxiang Zhao, Xiaochen Dong
Journal: Biomaterials (2022)
Biomineralized hydrogel DC vaccine for cancer immunotherapy: A boosting strategy via improving immunogenicity and reversing immune-inhibitory microenvironment
Authors: Wendi Huo, Xinjian Yang, Bei Wang, Lingzhi Cao, Ziyuan Fang, Zhenhua Li, Huifang Liu, Xing-jie Liang, Jinchao Zhang, Yi Jin
Journal: Biomaterials (2022)
RETRACTED: Atezolizumab, vemurafenib, and cobimetinib in patients with melanoma with CNS metastases (TRICOTEL): a multicentre, open-label, single-arm, phase 2 study
Authors: Reinhard Dummer, Paola Queirolo, Ana Maria Abajo Guijarro, Youyou Hu, Dao Wang, Sergio Jobim de Azevedo, Caroline Robert, Paolo Antonio Ascierto, Vanna Chiarion-Sileni, Paolo Pronzato, Francesco Spagnolo, Karmele Mujika Eizmendi, Gabriella Liszkay, Luis de la Cruz Merino, Hussein Tawbi
Journal: The Lancet Oncology (2022)
Artificial intelligence-based diagnosis of abnormalities in small-bowel capsule endoscopy
Authors: Zhen Ding, Huiying Shi, Hang Zhang, Hao Zhang, Shuxin Tian, Kun Zhang, Sicheng Cai, Fanhua Ming, Xiaoping Xie, Jun Liu, Rong Lin
Journal: Endoscopy (2022)

BACKGROUND : Further development of deep learning-based artificial intelligence (AI) technology to automatically diagnose multiple abnormalities in small-bowel capsule endoscopy (SBCE) videos is necessary. We aimed to develop an AI model, to compare its diagnostic performance with doctors of different experience levels, and to further evaluate its auxiliary role for doctors in diagnosing multiple abnormalities in SBCE videos. METHODS : The AI model was trained using 280 426 images from 2565 patients, and the diagnostic performance was validated in 240 videos. RESULTS : The sensitivity of the AI model for red spots, inflammation, blood content, vascular lesions, protruding lesions, parasites, diverticulum, and normal variants was 97.8 %, 96.1 %, 96.1 %, 94.7 %, 95.6 %, 100 %, 100 %, and 96.4 %, respectively. The specificity was 86.0 %, 75.3 %, 87.3 %, 77.8 %, 67.7 %, 97.5 %, 91.2 %, and 81.3 %, respectively. The accuracy was 95.0 %, 88.8 %, 89.2 %, 79.2 %, 80.8 %, 97.5 %, 91.3 %, and 93.3 %, respectively. For junior doctors, the assistance of the AI model increased the overall accuracy from 85.5 % to 97.9 % (P < 0.001, Bonferroni corrected), comparable to that of experts (96.6 %, P > 0.0125, Bonferroni corrected). CONCLUSIONS : This well-trained AI diagnostic model automatically diagnosed multiple small-bowel abnormalities simultaneously based on video-level recognition, with potential as an excellent auxiliary system for less-experienced endoscopists.
Correction: Impact of expert center endoscopic assessment of confirmed low grade dysplasia in Barrett’s esophagus diagnosed in community hospitals
Authors: Esther A. Nieuwenhuis, Sanne N. van Munster, Wouter L. Curvers, Bas L. A. M. Weusten, Lorenza Alvarez Herrero, Auke Bogte, Alaa Alkhalaf, B. Ed Schenk, Arjun D. Koch, Manon C. W. Spaander, Thjon J. Tang, Wouter B. Nagengast, Jessie Westerhof, Martin H. M. G. Houben, Jacques J.G.H.M. Bergman, Erik J. Schoon, Roos E. Pouw
Journal: Endoscopy (2022)

Correction to: Impact of expert center endoscopic assessment of confirmed low grade dysplasia in Barrett’s esophagus diagnosed in community hospitalsEndoscopy 2022; 54(10): 936-944DOI: 10.1055/a-1754-7309
An intricate interplay between stent drug dose and release rate dictates arterial restenosis
Authors: Alistair McQueen, Javier Escuer, André Fensterseifer Schmidt, Ankush Aggarwal, Simon Kennedy, Christopher McCormick, Keith Oldroyd, Sean McGinty
Journal: Journal of Controlled Release (2022)

Since the introduction of percutaneous coronary intervention (PCI) for the treatment of obstructive coronary artery disease (CAD), patient outcomes have progressively improved. Drug eluting stents (DES) that employ anti-proliferative drugs to limit excess tissue growth following stent deployment have proved revolutionary. However, restenosis and a need for repeat revascularisation still occurs after DES use. Over the last few years, computational models have emerged that detail restenosis following the deployment of a bare metal stent (BMS), focusing primarily on contributions from mechanics and fluid dynamics. However, none of the existing models adequately account for spatiotemporal delivery of drug and the influence of this on the cellular processes that drive restenosis. In an attempt to fill this void, a novel continuum restenosis model coupled with spatiotemporal drug delivery is presented. Our results indicate that the severity and time-course of restenosis is critically dependent on the drug delivery strategy. Specifically, we uncover an intricate interplay between initial drug loading, drug release rate and restenosis, indicating that it is not sufficient to simply ramp-up the drug dose or prolong the time course of drug release to improve stent efficacy. Our model also shows that the level of stent over-expansion and stent design features, such as inter-strut spacing and strut thickness, influence restenosis development, in agreement with trends observed in experimental and clinical studies. Moreover, other critical aspects of the model which dictate restenosis, including the drug binding site density are investigated, where comparisons are made between approaches which assume this to be either constant or proportional to the number of smooth muscle cells (SMCs). Taken together, our results highlight the necessity of incorporating these aspects of drug delivery in the pursuit of optimal DES design.
MESENTERIC EMBOLISM AND THROMBOSIS.A STUDY OF TWO HUNDRED AND FOURTEEN CASES.
Authors: JAMES MARSH JACKSON
Journal: JAMA (1904)

<h3>Case 8.</h3> —K. M., widow, age 60, admitted to the medical wards of the Johns Hopkins Hospital Jan. 14, 1898. Complained of pain in the stomach. <h3>Family History.</h3> —Unreported. <h3>Past History.</h3> —Had malaria many years ago. Rheumatism in right leg and arm two years ago. General health fair. Has done very hard work. Habits excellent. Bowels regular. Subject to slight dyspeptic attacks, with vomiting, off and on for seven years. Frequency of micturition. <h3>Present Illness.</h3> —Has not felt well for some months. About four weeks ago shortness of breath, from which she has suffered for years, grew worse, being very extreme on least exertion. Palpitation of heart, with dyspnea. Some swelling of feet. Pain and soreness in upper abdomen. Vomiting immediately after eating. On admission patient seemed in great distress. Slightly cyanotic. Lungs clear. Heart dullness not increased. Systolic murmur at apex. Pulse